Applied Environmental Metabolomics

Community Insights and Guidance from the Field

1st Edition - June 9, 2022
Editors: David J. Beale, Katie E. Hillyer, Andrew C. Warden, Oliver A.H. Jones
Language: English
Paperback ISBN:
9 7 8 - 0 - 1 2 - 8 1 6 4 6 0 - 0
eBook ISBN:
9 7 8 - 0 - 1 2 - 8 1 6 4 6 1 - 7

Applied Environmental Metabolomics: Community Insights and Guidance from the Field brings together contributions from global experts who have helped to define and develop the excit… Read more

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Applied Environmental Metabolomics: Community Insights and Guidance from the Field brings together contributions from global experts who have helped to define and develop the exciting and rapid advances that are taking place in the field of environmental metabolomics. This book is aimed at expert users, students, researchers, and academics in metabolomics and systems biology. It not only demonstrates the best practice in experimental design but also provides insight into state-of-the-art instrumentation and the depth of analysis one can expect to get by using various sampling, chromatographic, mass spectrometric, and nuclear magnetic resonance (NMR) techniques. Common experimental and technical pitfalls are also highlighted. This book provides a unique insight into the world of environmental metabolomics and will help the practicing scientist avoid repeating similar costly mistakes, steering them efficiently toward the generation of high-quality data and high-impact publications.

Cover
Title page
Table of Contents
Copyright
Contributors
Foreword
Part 1: Introduction
Chapter 1: Applied environmental metabolomics: Eliciting viewpoints from the metabolomics research community
Abstract
Introduction
Reports from the field
The future
References
Part 2: Reports from the field
Chapter 2: Measuring root exudate metabolites in holm oak (Quercus ilex) under drought and recovery
Abstract
Scope
Aims and objectives
Introduction
Approach (materials and methods)
Main findings
Summary and future perspectives
References
Chapter 3: Visualization of cyanogenic glycosides in floral tissues
Abstract
Acknowledgments
Scope
Aims and objectives of the study
Introduction
Approach (material and methods)
Sampling protocol
Analytical protocol
MALDI mass spectrometry imaging
Main findings
Quantification of floral cyanogenic glycoside concentrations
Identification of cyanogenic glycosides
Detection of cyanogenic glycosides in Proteaceae flowers using MALDI-MSI
What went right
What went wrong
Suggestions for improvements for future studies
Final remarks
References
Chapter 4: Environmental assessment of metal impacted soils using community metabolic profiling
Abstract
Scope
Aims and objectives
Introduction
Approach (materials and methods)
Main findings
Discussion
Final thoughts
References
Chapter 5: Decoding the metabolic landscape of maize responses to experimentally controlled drought stress: A greenhouse case study
Abstract
Scope
Aims and objectives
Introduction
Approach (material and methods)
Main findings
Concluding remarks—“What went right” and “what went wrong”
References
Chapter 6: Nontargeted screening of metabolites to discriminate disease suppressive and nonsuppressive soils for the fungal pathogen Rhizoctonia solani AG8
Abstract
Scope
Aims
Introduction
Approach
Main findings
Recommendations for agricultural field studies
Final remarks
References
Chapter 7: Ecosystem metabolomics of dissolved organic matter from arctic soil pore water across seasonal transitions
Abstract
Scope
Aims and objectives
Introduction
Approach
Main findings
Conclusion
References
Chapter 8: Temporal trends in metabolite profiles correspond with seasonal patterns of temperature and rainfall during field-scale ecotoxicology assessment
Abstract
Scope
Aims and objectives of the study
Introduction
Approach (materials and methods)
Main findings
What went right?
What would you recommend to other researchers wanting to do similar research?
What could be improved?
Final thoughts
References
Chapter 9: Metabolic responses of eelgrass (Zostera marina) to artificially induced stresses
Abstract
Scope
Aims and objectives
Introduction
Approach (material and methods)
Biological samples
Environment sampled
Sampling protocol
Herbicide exposure
Low light (dark) and high temperature
Growth, photosynthetic efficiency
Analytical protocol
Main findings
What went right
What went wrong
Summary and future perspectives
References
Chapter 10: Metabolomic profiling of anthropogenically threatened Australian seagrass Zostera muelleri using one- and two-dimensional gas chromatography
Abstract
Acknowledgment
Scope
Aims and objectives
Introduction
Experimental methods
Sample preparation
Metabolite profiling
Data preprocess and analysis
Main findings
What went wrong in seagrass metabolomics
What went right in seagrass metabolomics
Summary and future perspectives
References
Chapter 11: The metabolic response of marine copepods (Calanus spp.) to food deprivation, end-of-century ocean acidification, and global warming scenarios
Abstract
Acknowledgments
Scope
Aims and objectives of the study
Introduction
Approach (material and methods)
Biological sample
Environment sampled
Sampling protocol
Analytical protocol
Main findings
What went right?
What went wrong?
Summary and future perspectives
References
Further reading
Chapter 12: Untargeted screening of xenobiotics and metabolic profiles of green sea turtles on the Great Barrier Reef
Abstract
Scope
Aims and objectives
Introduction
Approach (material and methods)
Suggestions for future studies
Summary and future perspectives
References
Chapter 13: Butterflyfish gill mucus metabolome reflects diet preferences and gill parasite intensities
Abstract
Scope
Aims and objectives
Introduction
Approach (materials and methods)
Main findings
What went right
What went wrong
Summary and future perspectives
References
Chapter 14: Exploring the coral bleaching tipping point with 13C metabolomics
Abstract
Scope
Aims and objectives
Introduction
Approach (material and methods)
Main findings
What went well
What went wrong
What data did you wish you had but did not?
Summary and future perspectives
References
Chapter 15: The metabolic significance of symbiont community composition in the coral-algal symbiosis
Abstract
Scope
Aims and objectives
Introduction
Approach (materials and methods)
Main findings
What went right?
What went wrong?
Summary and future perspectives
References
Chapter 16: Evaluating the effects of environmental perturbations in bloom forming cyanobacteria through untargeted metabolomics
Abstract
Acknowledgments
Scope
Aims and objectives
Introduction
Approach (materials and methods)
Extraction and analytical protocols
Main findings
What went right
What went wrong
Suggestions and final remarks
References
Chapter 17: Metabolomics investigation into summer mortality events of Greenshell mussels (Perna canaliculus) in New Zealand
Abstract
Scope
Aim and objectives
Introduction
Approach (materials and methods)
Main findings
Summary and future perspectives
References
Chapter 18: Metabolic responses of the water flea (Daphnia magna) to individual contaminants and mixtures in presence of dissolved organic matter
Abstract
Scope
Aims and objectives of the studies
Introduction
Approach
Daphnia culturing and maintenance
Sublethal exposure to contaminants
Metabolite extraction
1H NMR data acquisition
Data processing and statistical analysis
Main findings
What went right
What went wrong
Suggestions for future studies
Conclusion
References
Chapter 19: NMR-based metabolomics of dragonfly nymphs exposed to multiple stressors: An approach for field assessments to diagnose effects
Abstract
Scope
Aims and objectives
Introduction
Approach (materials and methods)
Main findings
What went right?
What went wrong?
Summary and future perspectives
Final remarks
References
Chapter 20: Using laboratory-cultured nonbiting midge larvae (Chironomus tepperi) to identify early metabolic changes following exposure to zinc
Abstract
Scope
Aims and objectives
Introduction
Approach (materials and methods)
Main findings
What worked
What did not work
Future studies
Summary
References
Chapter 21: Using field-collected estuarine worms to identify early metabolic changes following exposure to zinc
Abstract
Scope
Aims and objectives
Introduction
Approach
Main findings
What worked
What didn’t work
Future perspectives
Summary
References
Chapter 22: Metabolomic signatures of Naegleria fowleri colonization in drinking water distribution systems in rural Western Australia
Abstract
Scope
Aim and objectives of the study
Introduction
Approach (materials and methods)
Summary of project outcomes and primary finding
What went wrong?
What went right?
Concluding remarks
References
Chapter 23: Establishing a regional microbial blueprint of metabolic function in sediment collected from pristine tropical estuarine systems
Abstract
Scope
Aims and objectives
Introduction
Approach (material and methods)
Analytical protocol
Main findings
Concluding remarks
References
Chapter 24: Acute sublethal exposure to a neonicotinoid pesticide triggers a short-term metabolic response in honey bee larvae
Abstract
Scope
Aims and objectives
Introduction
Approach (materials and methods)
Main findings
Concluding comments
References
Part 3: Future perspectives
Chapter 25: Community insights and guidance from the field
Abstract
Introduction
Case study contributions
Community insights
Conclusions and final remarks
References
Chapter 26: The future of environmental metabolomics
Abstract
Introduction
Risk assessment and metabolomics
Flux analysis
Community metabolomics
Technological development
Systems toxicology
Summary
References
Index

David J. Beale

Dr David J. Beale is a Senior Research Scientist at the CSIRO, delivering research outcomes and creating impact in the area of environmental metabolomics and analytical chemistry. David couples high-throughput next-generation tools with environmental monitoring techniques for detecting, quantifying and tracking contaminants in the environment and assessing their biological impact using omics-based approaches. David is the current vice president of the Australian and New Zealand Metabolomics Network.

Affiliations and expertise

Senior Research Scientist, Metabolomics and Proteomics Team, Land and Water, CSIRO, Australia

Katie E. Hillyer

Katie is a marine biologist by trade, interested in the application of total systems biology-based approaches to answer ecologically relevant questions (environmental 'omics). Specifically, the development and use of these sensitive tools for assessing complex changes (natural and man-made) in aquatic ecosystems, and ultimately to enhancing system management, function and resilience.

Affiliations and expertise

CSIRO Land and Water, Dutton Park, Brisbane, Australia

Andrew C. Warden

Dr Warden leads the CSIRO Metabolomics & Proteomics Team at CSIRO and is based in Canberra, Australia. He obtained his PhD in Chemistry from Monash University, Victoria, Australia in 2005 after which he joined CSIRO (Melbourne) as postdoctoral fellow. He moved to Canberra in 2007 and gained tenure as a research scientist at CSIRO in 2011 after completing a second postdoctoral fellowship. Dr Warden has worked across a very broad range of science areas, including synthetic organic chemistry, X-ray crystallography, novel lipid production in plants, enzyme design and engineering, biofuels and bioenergy, molecular modelling and computational chemistry. His most recent efforts have been in omics since leading the Metabolomics and Proteomics Team into the space over the past few years. He has led the effort to build a world class analytical chemistry facility at CSIRO Black Mountain since 2012 and sits on the Steering Committee for the Joint Mass Spectrometry Facility at the Australian National University (ANU). Dr Warden also leads the Metabolomics arm of the CSIRO/ANU National Agricultural and Environmental Sciences Precinct, which is a $48M endeavour between the two organisations to build a collaborative hub to build a sustainable future for the environment, agriculture and global food supplies.

Affiliations and expertise

Senior Research Scientist, Team Leader, Metabolomics and Proteomics Team, Land and Water, CSIRO, Australia

Oliver A.H. Jones

Oliver Jones is a Professor of analytical chemistry at RMIT University in Melbourne, Australia. He obtained his PhD from Imperial College London in 2005, after which he joined the University of Cambridge as a postdoctoral fellow in Biochemistry until 2009. He then worked as a lecturer at the University of Durham before moving to RMIT in 2012. Prof. Jones is currently the Associate Dean for Biosciences and Food Technology at RMIT. He has broad interdisciplinary interests across many areas of chemistry, (analytical, biological, environmental) and chemical/environmental engineering (water technology and hydrology). Prof. Jones is particularly interested in tracking the fate and behaviour of organic micropollutants in the environment and determining their possible effects on biological systems. He previously served two terms as a Director of the International Metabolomics Society and was a past president of the Australian and New Zealand Metabolomics Network, co-president of Proteomics and Metabolomics Victoria, and secretary of the Australian and New Zealand Society for Magnetic Resonance as well as a member the Australian Academy of Science, National Committee for Chemistry. He is a Fellow of the Royal Society of Chemistry and the Royal Australian Chemical Institute, and an Associate Fellow of the Institution for Chemical Engineers.

Affiliations and expertise

Professor, School of Science, RMIT University, Australia

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Applied Environmental Metabolomics

Community Insights and Guidance from the Field

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Save 50% on book bundles

Institutional subscription on ScienceDirect

David J. Beale

Katie E. Hillyer

Andrew C. Warden

Oliver A.H. Jones